[gmx-users] Unnatural amino acid MD
ajogale at emory.edu
Mon Mar 6 18:22:55 CET 2006
I am trying to do MD on a peptide with an unnatural amino acid, and i
have duly modified the OPLS forcefield .hdb, .rtp, and aminoacid.dat
file accordingly. Now, when I am trying to do the grompp for the
energy minimization, the program is asking me to put parameters for
the dihedrals in the .top file. I did put most of them in, but cannot
find values for the other ones. More importantly, some of the
dihedrals don't make sense, because they don't seem to have anything
to do with keeping an aromatic ring flat, for example. A few improper
dihedrals should suffice for my amino acid, which is phenylglycine.
But the ones that the program is asking me to put in seem to
correspond to quite obscure atom combinations. Is this a problem with
gromacs, or with the OPLS force field that I am using?
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